X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=025a7a085ef9e69e1845731f57ebbc8156fb7ad4;hb=bdbd32582db88724697211a25b08f9cb8958bcb1;hp=cc303d65e21308178bd79cd596701250d85897e8;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index cc303d6..025a7a0 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -21,6 +21,7 @@
 package jalview.schemes;
 
 import jalview.datamodel.AnnotatedCollectionI;
+import jalview.util.ColorUtils;
 
 import java.awt.Color;
 
@@ -415,8 +416,7 @@ public class ColourSchemeProperty
         try
         {
           // fix the launchApp user defined coloursheme transfer bug
-          jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
-                  "white");
+          UserColourScheme ucs = new UserColourScheme("white");
           ucs.parseAppletParameter(name);
 
         } catch (Exception e)
@@ -442,8 +442,7 @@ public class ColourSchemeProperty
    * @return null or an instance of the colourscheme configured to colour given
    *         sequence set
    */
-  public static ColourSchemeI getColour(
-          jalview.datamodel.AnnotatedCollectionI coll, int index)
+  public static ColourSchemeI getColour(AnnotatedCollectionI coll, int index)
   {
     // TODO 3.0 2.8 refactor signature to take an alignmentI like container so
     // colourschemes based on annotation can be initialised
@@ -597,4 +596,32 @@ public class ColourSchemeProperty
 
     return col;
   }
+
+  public static Color rnaHelices[] = null;
+
+  public static void initRnaHelicesShading(int n)
+  {
+    int j = 0;
+    if (rnaHelices == null)
+    {
+      rnaHelices = new Color[n + 1];
+    }
+    else if (rnaHelices != null && rnaHelices.length <= n)
+    {
+      Color[] t = new Color[n + 1];
+      System.arraycopy(rnaHelices, 0, t, 0, rnaHelices.length);
+      j = rnaHelices.length;
+      rnaHelices = t;
+    }
+    else
+    {
+      return;
+    }
+    // Generate random colors and store
+    for (; j <= n; j++)
+    {
+      rnaHelices[j] = ColorUtils.generateRandomColor(Color.white);
+    }
+  }
+
 }